Becksteinlab's repositories
propka
PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
SAMPL6_logP_data
Supplementary data for SAMPL6 Part II (logP) calculations.
lipidbook
Lipidbook force field repository (public issue tracker and wiki).
scipy2019-pmda-data
data and abstract for PMDA paper (SciPy 2019)
workflows-talk
Materials for workflows/automation talks.
workshop_testing
Files for the summer workshop for tests and CI
AdKGromacsTutorial
Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
queuetools
a collection of tools that make a distributed, heterogeneous workstation queue easier to leverage
queuing-systems
Demo files for queuing systems talk
Parallel-analysis-in-the-MDAnalysis-Library
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
MDAnalysis-with-Dask
Benchmarking MDAnalysis with dask.
gromacswrapper.analysis
Legacy code from GromacsWrapper: gromacs.analysis module
remote-vmd
Python client for the VMD server.
conda-gromacs-2016
Conda package of gromacs 2016 intended for testing purposes.
conda-gromacs-4.6.7
Conda package of gromacs 4.6.7 intended for testing purposes.
conda-gromacs-5.1.2
Conda package of gromacs 5.1.2 intended for testing purposes.
minlatex
A minimal working example for an article written in LaTeX
MDAnalysis-workshop
MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop
vesicle_library
library of vesicles with the Dry Martini force field
SPIDAL-www
DSC-Spidal Web Page
ComputationalPhysics_PHY494
Materials for PHY 494
beckernels
A repository of radical.ensemblemd kernels used by the Beckstein Lab
PSAnalysisTutorial
Examples and data for performing path similarity analysis (PSA).
making-prettier-plots
a quick primer on making prettier (and more impactful) plots